Title: STRUctural Modeling of Latent Variables for General Pedigree
Diff between strum versions 0.4 dated 2014-07-03 and 0.5 dated 2014-12-10
Description: This package implements a broad class of latent variable and structural equation models for general pedigree data.
Author: Nathan Morris [aut, cre],
Yeunjoo Song [aut],
Stephen Cahn [ctb]
Maintainer: Nathan Morris
ChangeLog | 8 ++++++++
DESCRIPTION | 10 +++++-----
MD5 | 24 ++++++++++++------------
NAMESPACE | 4 +++-
R/fitModel.R | 6 +++++-
build/vignette.rds |binary
inst/doc/strum-example.Rnw | 6 +++---
inst/doc/strum-example.pdf |binary
inst/doc/strum-intro.Rnw | 2 +-
inst/doc/strum-intro.pdf |binary
man/strum-package.Rd | 4 ++--
vignettes/strum-example.Rnw | 6 +++---
vignettes/strum-intro.Rnw | 2 +-
13 files changed, 43 insertions(+), 29 deletions(-)
Title: Fitting Routines for the Vitality Family of Mortality Models
Diff between vitality versions 1.0 dated 2013-02-11 and 1.1 dated 2014-12-10
Description: Provides fitting routines for four versions of the
Vitality family of mortality models.
Author: Gregor Passolt, James J. Anderson, Ting Li, David H. Salinger, David J. Sharrow
Maintainer: David J. Sharrow
vitality-1.0/vitality/R/vitality.2ps.R |only
vitality-1.0/vitality/man/SurvFn.2ps.Rd |only
vitality-1.0/vitality/man/SurvFn.h.Rd |only
vitality-1.0/vitality/man/ft.Rd |only
vitality-1.0/vitality/man/logLikelihood.2ps.Rd |only
vitality-1.0/vitality/man/mu.vd.Rd |only
vitality-1.0/vitality/man/mu.vd1.Rd |only
vitality-1.0/vitality/man/mu.vd2.Rd |only
vitality-1.0/vitality/man/plotting.2ps.Rd |only
vitality-1.0/vitality/man/stdErr.2ps.Rd |only
vitality-1.0/vitality/man/survProbInc.2ps.Rd |only
vitality-1.0/vitality/man/vft.Rd |only
vitality-1.0/vitality/man/vitality.2ps.Rd |only
vitality-1.1/vitality/DESCRIPTION | 25 +-
vitality-1.1/vitality/MD5 | 77 ++++++--
vitality-1.1/vitality/NAMESPACE | 9 -
vitality-1.1/vitality/R/data_documentation.R | 27 +--
vitality-1.1/vitality/R/density.R | 89 ++++++----
vitality-1.1/vitality/R/mortality_rate.R | 140 ++++++++++-----
vitality-1.1/vitality/R/package_documentation.R | 88 +++++-----
vitality-1.1/vitality/R/vitality.4p.R |only
vitality-1.1/vitality/R/vitality.6p.R |only
vitality-1.1/vitality/R/vitality.k.R |only
vitality-1.1/vitality/R/vitality.ku.R |only
vitality-1.1/vitality/data/rainbow_trout_for_k.rda |only
vitality-1.1/vitality/data/swedish_females.rda |binary
vitality-1.1/vitality/man/SurvFn.4p.Rd |only
vitality-1.1/vitality/man/SurvFn.6p.Rd |only
vitality-1.1/vitality/man/SurvFn.h.4p.Rd |only
vitality-1.1/vitality/man/SurvFn.h.6p.Rd |only
vitality-1.1/vitality/man/SurvFn.k.Rd |only
vitality-1.1/vitality/man/SurvFn.ku.Rd |only
vitality-1.1/vitality/man/dataPrep.Rd | 65 +++----
vitality-1.1/vitality/man/ft.4p.Rd |only
vitality-1.1/vitality/man/ft.6p.Rd |only
vitality-1.1/vitality/man/indexFinder.Rd | 37 ++--
vitality-1.1/vitality/man/logLikelihood.4p.Rd |only
vitality-1.1/vitality/man/logLikelihood.6p.Rd |only
vitality-1.1/vitality/man/logLikelihood.k.Rd |only
vitality-1.1/vitality/man/logLikelihood.ku.Rd |only
vitality-1.1/vitality/man/mu.vd.4p.Rd |only
vitality-1.1/vitality/man/mu.vd.6p.Rd |only
vitality-1.1/vitality/man/mu.vd1.4p.Rd |only
vitality-1.1/vitality/man/mu.vd1.6p.Rd |only
vitality-1.1/vitality/man/mu.vd2.4p.Rd |only
vitality-1.1/vitality/man/mu.vd2.6p.Rd |only
vitality-1.1/vitality/man/plotting.4p.Rd |only
vitality-1.1/vitality/man/plotting.6p.Rd |only
vitality-1.1/vitality/man/plotting.k.Rd |only
vitality-1.1/vitality/man/plotting.ku.Rd |only
vitality-1.1/vitality/man/rainbow_trout_for_k.Rd |only
vitality-1.1/vitality/man/stdErr.4p.Rd |only
vitality-1.1/vitality/man/stdErr.6p.Rd |only
vitality-1.1/vitality/man/stdErr.k.Rd |only
vitality-1.1/vitality/man/stdErr.ku.Rd |only
vitality-1.1/vitality/man/survProbInc.4p.Rd |only
vitality-1.1/vitality/man/survProbInc.6p.Rd |only
vitality-1.1/vitality/man/survProbInc.k.Rd |only
vitality-1.1/vitality/man/survProbInc.ku.Rd |only
vitality-1.1/vitality/man/swedish_females.Rd | 29 +--
vitality-1.1/vitality/man/vft.4p.Rd |only
vitality-1.1/vitality/man/vft.6p.Rd |only
vitality-1.1/vitality/man/vitality.4p.Rd |only
vitality-1.1/vitality/man/vitality.6p.Rd |only
vitality-1.1/vitality/man/vitality.Rd | 184 +++++++++++++++------
vitality-1.1/vitality/man/vitality.k.Rd |only
vitality-1.1/vitality/man/vitality.ku.Rd |only
67 files changed, 482 insertions(+), 288 deletions(-)
Title: Identify and visualize significantly responsive branches in a
phylogenetic tree
Diff between SigTree versions 1.6 dated 2014-07-15 and 1.7 dated 2014-12-10
Description: SigTree takes a phylogenetic tree (of class phylo) and a data frame (or matrix) of corresponding tip labels and p-values and determines the significance of the branches (families of p-values) and plots the tree with colored branches (corresponding to families) according to their levels of significance. Also produces a CSV file with the p-values of all of the branches as well as which tips belong to which branches. Finally, it exports a file that can be opened in FigTree that produces a colored plot (colored branches according to their significance of corresponding groups of p-values) with p-value annotations.
Author: John R. Stevens and Todd R. Jones
Maintainer: John R. Stevens
DESCRIPTION | 8 ++++----
MD5 | 26 +++++++++++++-------------
NEWS | 19 +++++++++++++++++++
build/vignette.rds |binary
inst/CITATION | 8 ++++----
inst/doc/SigTree.R | 8 ++++----
inst/doc/SigTree.Rnw | 47 +++++++++++++++++++++++++++++++++++++----------
inst/doc/SigTree.pdf |binary
man/SigTree-package.Rd | 6 +++---
man/SigTree.other.Rd | 2 +-
man/export.figtree.Rd | 2 +-
man/export.inherit.Rd | 2 +-
man/plotSigTree.Rd | 2 +-
vignettes/SigTree.Rnw | 47 +++++++++++++++++++++++++++++++++++++----------
14 files changed, 125 insertions(+), 52 deletions(-)
Title: Risk regression models for survival analysis with competing
risks
Diff between riskRegression versions 1.0.9 dated 2014-12-05 and 1.1.1 dated 2014-12-10
More information about riskRegression at CRAN
Description: Risk regression models for survival analysis with and without
competing risks.
Author: Thomas Alexander Gerds, Thomas Harder Scheike
Maintainer: Thomas Alexander Gerds
DESCRIPTION | 6 -
MD5 | 10 +--
R/predict.FGR.R | 3
R/riskRegression.R | 4 -
src/matrix.c | 149 ++++++++++++++++++++++++++++++++++++++-----------
tests/testthat/brier.R | 2
6 files changed, 133 insertions(+), 41 deletions(-)
Permanent link
Title: R for Amplicon-based Metagenomics
Diff between RAM versions 1.1.0 dated 2014-10-22 and 1.2.0 dated 2014-12-10
Description: This package provides a series of functions to make amplicon-based metagenomic analysis more accessible, and publication-quality plots simple. Amplicon-based (or targeted) metagenomics amplifies and sequences selected DNA regions of environmental samples, but not the entire pool of genetic material, which is referred to as shotgun metagenomics. The amplicon-metagenomics mainly aims at characterizing broad microbiota biodiversity in different environments.
Author: Wen Chen and Joshua Simpson
Maintainer: Wen Chen
RAM-1.1.0/RAM/R/dissim_functions.R |only
RAM-1.1.0/RAM/R/diversity_indices.R |only
RAM-1.1.0/RAM/R/read_files.R |only
RAM-1.1.0/RAM/R/utility_functions.R |only
RAM-1.1.0/RAM/R/write_files.R |only
RAM-1.1.0/RAM/man/write.OTU.Rd |only
RAM-1.1.0/RAM/tests |only
RAM-1.2.0/RAM/ChangeLog | 203 ++++
RAM-1.2.0/RAM/DESCRIPTION | 16
RAM-1.2.0/RAM/MD5 | 146 ++-
RAM-1.2.0/RAM/NAMESPACE | 13
RAM-1.2.0/RAM/NEWS | 172 ++++
RAM-1.2.0/RAM/R/assist.ado.R |only
RAM-1.2.0/RAM/R/assist_NB.R |only
RAM-1.2.0/RAM/R/core.R | 885 ++++++++++++++-------
RAM-1.2.0/RAM/R/dissim_functions_plot.R | 625 +++++++++-----
RAM-1.2.0/RAM/R/group.Taxa.R |only
RAM-1.2.0/RAM/R/group_CLUST.R |only
RAM-1.2.0/RAM/R/internal_functions.R | 44 -
RAM-1.2.0/RAM/R/metadata.R | 597 +++++++++++++-
RAM-1.2.0/RAM/R/ordination_functions.R | 1251 +++++++++++++++++++++++++++++-
RAM-1.2.0/RAM/R/plot_heatmaps.R | 284 ++++--
RAM-1.2.0/RAM/R/plot_misc.R | 1000 ++++++++---------------
RAM-1.2.0/RAM/R/process_data.R | 566 +++++++++----
RAM-1.2.0/RAM/R/read_and_write_files.R |only
RAM-1.2.0/RAM/R/summary.R |only
RAM-1.2.0/RAM/R/taxonomy_functions.R | 215 ++++-
RAM-1.2.0/RAM/R/theme_ggplot.R |only
RAM-1.2.0/RAM/R/utility_function.R |only
RAM-1.2.0/RAM/R/validation_functions.R | 59 +
RAM-1.2.0/RAM/build/RAM.pdf |binary
RAM-1.2.0/RAM/inst/CITATION | 27
RAM-1.2.0/RAM/man/LCA.OTU.Rd | 26
RAM-1.2.0/RAM/man/META.clust.Rd |only
RAM-1.2.0/RAM/man/OTU.diversity.Rd | 30
RAM-1.2.0/RAM/man/OTU.ord.Rd |only
RAM-1.2.0/RAM/man/OTU.rarefy.Rd |only
RAM-1.2.0/RAM/man/OTU.recap.Rd | 60 -
RAM-1.2.0/RAM/man/OTU.subsets.Rd | 59 -
RAM-1.2.0/RAM/man/RAM-package.Rd | 33
RAM-1.2.0/RAM/man/RAM.input.formatting.Rd |only
RAM-1.2.0/RAM/man/RAM.pal.Rd |only
RAM-1.2.0/RAM/man/Taxa.ord.Rd |only
RAM-1.2.0/RAM/man/assist.NB.Rd |only
RAM-1.2.0/RAM/man/assist.ado.Rd |only
RAM-1.2.0/RAM/man/assist.ordination.Rd | 10
RAM-1.2.0/RAM/man/col.splitup.Rd | 11
RAM-1.2.0/RAM/man/combine.OTU.Rd |only
RAM-1.2.0/RAM/man/core.OTU.Rd | 19
RAM-1.2.0/RAM/man/core.OTU.rank.Rd |only
RAM-1.2.0/RAM/man/core.Taxa.Rd | 29
RAM-1.2.0/RAM/man/correlation.Rd | 14
RAM-1.2.0/RAM/man/data.clust.Rd |only
RAM-1.2.0/RAM/man/data.revamp.Rd |only
RAM-1.2.0/RAM/man/dissim.Rd | 61 -
RAM-1.2.0/RAM/man/dissim.heatmap.Rd | 14
RAM-1.2.0/RAM/man/dissim.plot.Rd | 107 +-
RAM-1.2.0/RAM/man/diversity.indices.Rd | 25
RAM-1.2.0/RAM/man/envis.NB.Rd |only
RAM-1.2.0/RAM/man/filter.META.Rd |only
RAM-1.2.0/RAM/man/filter.OTU.Rd | 36
RAM-1.2.0/RAM/man/filter.Taxa.Rd |only
RAM-1.2.0/RAM/man/fread.OTU.Rd |only
RAM-1.2.0/RAM/man/fread.meta.Rd |only
RAM-1.2.0/RAM/man/group.OTU.Rd | 43 -
RAM-1.2.0/RAM/man/group.Taxa.bar.Rd |only
RAM-1.2.0/RAM/man/group.Taxa.box.Rd |only
RAM-1.2.0/RAM/man/group.abund.Taxa.Rd |only
RAM-1.2.0/RAM/man/group.abundance.Rd | 33
RAM-1.2.0/RAM/man/group.diversity.Rd |only
RAM-1.2.0/RAM/man/group.heatmap.Rd | 65 +
RAM-1.2.0/RAM/man/group.heatmap.simple.Rd | 15
RAM-1.2.0/RAM/man/group.indicators.Rd | 60 +
RAM-1.2.0/RAM/man/group.rich.Rd |only
RAM-1.2.0/RAM/man/group.spatial.Rd | 3
RAM-1.2.0/RAM/man/group.spec.Rd |only
RAM-1.2.0/RAM/man/group.venn.Rd |only
RAM-1.2.0/RAM/man/match.data.Rd |only
RAM-1.2.0/RAM/man/pcoa.plot.Rd | 42 -
RAM-1.2.0/RAM/man/percent.classified.Rd | 11
RAM-1.2.0/RAM/man/read.OTU.Rd | 6
RAM-1.2.0/RAM/man/read.meta.Rd | 10
RAM-1.2.0/RAM/man/reset.META.Rd | 15
RAM-1.2.0/RAM/man/sample.locations.Rd | 2
RAM-1.2.0/RAM/man/sample.map.Rd |only
RAM-1.2.0/RAM/man/sample.sites.Rd |only
RAM-1.2.0/RAM/man/shared.OTU.Rd | 12
RAM-1.2.0/RAM/man/shared.Taxa.Rd |only
RAM-1.2.0/RAM/man/tax.fill.Rd | 8
RAM-1.2.0/RAM/man/theme_ggplot.Rd |only
RAM-1.2.0/RAM/man/top.groups.plot.Rd | 37
RAM-1.2.0/RAM/man/transpose.LCA.Rd |only
RAM-1.2.0/RAM/man/valid.taxonomy.Rd |only
RAM-1.2.0/RAM/man/write.data.Rd |only
94 files changed, 5083 insertions(+), 1916 deletions(-)
Title: Product-limit estimation for censored event history analysis
Diff between prodlim versions 1.5.0 dated 2014-12-05 and 1.5.1 dated 2014-12-10
Description: Fast and user friendly implementation of nonparametric estimators
for censored event history (survival) analysis. Kaplan-Meier and
Aalen-Johansen method.
Author: Thomas A. Gerds
Maintainer: Thomas A. Gerds
DESCRIPTION | 6 -
MD5 | 31 +++---
R/atRisk.R | 20 ++--
R/confInt.R | 2
R/jackknife.R | 92 ++++---------------
R/plot.prodlim.R | 227 +++++++++++++++++++++++++++++++------------------
R/predict.prodlim.R | 20 ++--
R/prodlim.R | 23 +++-
R/summary.prodlim.R | 100 ++++++++++++++++-----
man/atRisk.Rd | 2
man/confInt.Rd | 2
man/jackknife.Rd | 54 -----------
man/plot.prodlim.Rd | 92 +++++++++++--------
man/prodlim.Rd | 2
man/summary.prodlim.Rd | 85 +++++++++++++++---
tests |only
16 files changed, 432 insertions(+), 326 deletions(-)
Title: Physical activity with accelerometers
Diff between pawacc versions 1.2 dated 2014-06-20 and 1.2.1 dated 2014-12-10
Description: Process, format and store accelerometer data
Author: Marco Geraci
Maintainer: Marco Geraci
DESCRIPTION | 10 +++++-----
MD5 | 6 +++---
inst/ChangeLog | 6 ++++++
man/pawacc-package.Rd | 4 ++--
4 files changed, 16 insertions(+), 10 deletions(-)
Title: Model Based Clustering, Classification and Discriminant Analysis
Using the Mixture of Generalized Hyperbolic Distributions
Diff between MixGHD versions 1.1 dated 2014-10-22 and 1.2 dated 2014-12-10
Description: Carries out model-based clustering, classification and discriminant analysis using five different models. The models are all based on the generalized hyperbolic distribution.The first model MGHD is the classical mixture of generalized hyperbolic distributions. The MGHFA is the mixture of generalized hyperbolic factor analyzers for high dimensional data sets. The MSGHD, mixture of multiple scaled generalized hyperbolic distributions. The cMSGHD is a MSGHD with convex contour plots. The MCGHD, mixture of coalesced generalized hyperbolic distributions is a new more flexible model.
Author: Cristina Tortora, Ryan P. Browne, Brian C. Franczak and Paul D. McNicholas.
Maintainer: Cristina Tortora
DESCRIPTION | 14 +++++-----
MD5 | 32 +++++++++++------------
R/DA.R | 36 +++++++++++++-------------
R/GHD.R | 38 +++++++++++++--------------
R/MCGHD.R | 9 ++++--
R/MGHD.R | 9 ++++--
R/MGHFA.R | 8 ++++-
R/MSGHD.R | 9 ++++--
R/Selection.R | 76 +++++++++++++++++++++++++++++++++++++++++++++++++------
R/cMSGHD.R | 9 ++++--
man/DA.Rd | 16 ++++++-----
man/MCGHD.Rd | 5 ++-
man/MGHD.Rd | 4 ++
man/MGHFA.Rd | 6 ++--
man/MSGHD.Rd | 4 ++
man/Selection.Rd | 18 +++++++------
man/cMSGHD.Rd | 6 ++--
17 files changed, 196 insertions(+), 103 deletions(-)
Title: Full Interactive GUI for Dynamic Biplot in R
Diff between dynBiplotGUI versions 1.1.1 dated 2014-10-30 and 1.1.2 dated 2014-12-10
Description: A GUI to solve dynamic biplots and classical biplot. Try matrices of 2-way and 3-way. The GUI can be run in multiple languages.
Author: Jaime Egido [aut, cre]
Maintainer: Jaime Egido
ChangeLog | 10 +++
DESCRIPTION | 10 +--
MD5 | 10 +--
R/dynBiplot.R | 115 +++++++++++++++++++++++---------------------
man/dynBiplot.Rd | 2
man/dynBiplotGUI-package.Rd | 2
6 files changed, 84 insertions(+), 65 deletions(-)
Title: Dunn's Test Of Multiple Comparisons Using Rank Sums
Diff between dunn.test versions 1.2.0 dated 2014-09-10 and 1.2.1 dated 2014-12-10
Description: Computes Dunn's test (1964) for stochastic dominance and reports the results among multiple pairwise comparisons after a Kruskal-Wallis test for stochastic dominance among k groups (Kruskal and Wallis, 1952). The interpretation of stochastic dominance requires an assumption that the CDF of one group does not cross the CDF of the other. dunn.test makes k(k-1)/2 multiple pairwise comparisons based on Dunn's z-test-statistic approximations to the actual rank statistics. The null hypothesis for each pairwise comparison is that the probability of observing a randomly selected value from the first group that is larger than a randomly selected value from the second group equals one half; this null hypothesis corresponds to that of the Wilcoxon-Mann-Whitney rank-sum test. Like the rank-sum test, if the data can be assumed to be continuous, and the distributions are assumed identical except for a difference in location, Dunn's test may be understood as a test for median difference. dunn.test accounts for tied ranks.
Author: Alexis Dinno
Maintainer: Alexis Dinno
DESCRIPTION | 12 ++++++------
MD5 | 4 ++--
man/dunn.test.Rd | 2 ++
3 files changed, 10 insertions(+), 8 deletions(-)
Title: Distance-Based Statistics
Diff between dbstats versions 1.0.3 dated 2013-11-21 and 1.0.4 dated 2014-12-10
Description: Prediction methods where explanatory information is coded as a matrix of distances between individuals. Distances can either be directly input as a distances matrix, a squared distances matrix, an inner-products matrix or computed from observed predictors.
Author: Boj, Eva
Maintainer: Josep Fortiana
DESCRIPTION | 14 +++++-----
MD5 | 31 ++++++++++++-----------
NAMESPACE | 3 ++
NEWS | 9 ++++++
R/dbglm_iteration.r | 9 +++++-
R/ldbglm.r | 10 ++-----
R/print.summary.ldbglm.r |only
R/print.summary.ldblm.r | 63 +++++++++++++++++++++++------------------------
R/summary.ldbglm.r |only
R/summary.ldblm.r | 21 +++++----------
man/dbglm.Rd | 2 -
man/dblm.Rd | 4 +-
man/dbplsr.Rd | 5 +--
man/dbstats-package.Rd | 4 +-
man/ldbglm.Rd | 4 +-
man/ldblm.Rd | 2 -
man/summary.ldbglm.rd |only
man/summary.ldblm.rd | 10 ++-----
18 files changed, 100 insertions(+), 91 deletions(-)
Title: Robust Cronbach's Alpha and Mcdonald's Omega with Missing and
Non-normal Data
Diff between coefficientalpha versions 0.3.2 dated 2014-11-14 and 0.3.3 dated 2014-12-10
More information about coefficientalpha at CRAN
Description: Cronbach's alpha and McDonald's omega are widely used reliability or internal consistency measures in social, behavioral and education sciences. Alpha is reported in nearly every study that involves measuring a construct through multiple test items. The package coefficientalpha calculates coefficient alpha and omega with missing data and non-normal data. Robust standard errors and confidence intervals are also provided. A test is also available to test the tau-equivalent and homogeneous assumptions.
Author: Zhiyong Zhang and Ke-Hai Yuan
Maintainer: Zhiyong Zhang
DESCRIPTION | 6 +++---
MD5 | 7 ++++---
R/Cronbach.R | 22 ++++++++++++----------
data/example.txt.gz |binary
inst |only
5 files changed, 19 insertions(+), 16 deletions(-)
Permanent link
Title: A collection of miscellaneous tools for reproducible research
with R.
Diff between repmis versions 0.3 dated 2014-09-18 and 0.3.3 dated 2014-12-10
Description: The package includes tools to load R packages
and automatically generate BibTeX files citing them as well as load
plain-text and Excel formatted data stored on Dropbox, GitHub, and from
other sources.
Author: Christopher Gandrud
Maintainer: Christopher Gandrud
DESCRIPTION | 8 ++---
MD5 | 26 +++++++++--------
NAMESPACE | 4 +-
NEWS | 59 +++++++++++++++++++++++++++++---------
R/InstallOldPackages.R | 70 +++++++++++++++++++++++-----------------------
R/git_stamp.R |only
R/scan_https.R |only
R/utils.R | 31 ++++++++++----------
README.md | 16 +++++++---
man/InstallOldPackages.Rd | 2 -
man/LoadandCite.Rd | 2 -
man/git_stamp.Rd |only
man/scan_https.Rd |only
man/source_DropboxData.Rd | 2 -
man/source_XlsxData.Rd | 2 -
man/source_data.Rd | 2 -
16 files changed, 135 insertions(+), 89 deletions(-)
Title: Dirichlet Regression in R
Diff between DirichletReg versions 0.5-2 dated 2014-09-18 and 0.6-1 dated 2014-12-10
Description: Implements the Dirichlet Regression in R
Author: Marco Johannes Maier [cre, aut]
Maintainer: Marco Johannes Maier
DirichletReg-0.5-2/DirichletReg/inst/NEWSRd2txt.R |only
DirichletReg-0.5-2/DirichletReg/src/dirichlet.c |only
DirichletReg-0.5-2/DirichletReg/tests/testthat/test-ArcticTests.R |only
DirichletReg-0.5-2/DirichletReg/vignettes/_compile.bat |only
DirichletReg-0.6-1/DirichletReg/.Rinstignore | 7
DirichletReg-0.6-1/DirichletReg/DESCRIPTION | 15
DirichletReg-0.6-1/DirichletReg/MD5 | 119 -
DirichletReg-0.6-1/DirichletReg/NAMESPACE | 83
DirichletReg-0.6-1/DirichletReg/NEWS | 39
DirichletReg-0.6-1/DirichletReg/R/AIC.DirichletRegModel.R | 2
DirichletReg-0.6-1/DirichletReg/R/DR_LL_alt.R | 266 +--
DirichletReg-0.6-1/DirichletReg/R/DR_LL_common.R | 66
DirichletReg-0.6-1/DirichletReg/R/DR_data.R | 224 +-
DirichletReg-0.6-1/DirichletReg/R/DirichReg.R | 173 +-
DirichletReg-0.6-1/DirichletReg/R/DirichReg_fit.R | 78
DirichletReg-0.6-1/DirichletReg/R/Dirichlet.R | 62
DirichletReg-0.6-1/DirichletReg/R/anova.DirichletRegModel.R | 26
DirichletReg-0.6-1/DirichletReg/R/cmyk2rgb.R | 2
DirichletReg-0.6-1/DirichletReg/R/coef.DirichletRegModel.R | 2
DirichletReg-0.6-1/DirichletReg/R/confint.DirichletRegModel.R | 44
DirichletReg-0.6-1/DirichletReg/R/coord.trafo.R | 10
DirichletReg-0.6-1/DirichletReg/R/drop1.DirichletRegModel.R |only
DirichletReg-0.6-1/DirichletReg/R/fitted.DirichletRegModel.R | 2
DirichletReg-0.6-1/DirichletReg/R/get_starting_values.R | 108 -
DirichletReg-0.6-1/DirichletReg/R/lines.DirichletRegData.R | 18
DirichletReg-0.6-1/DirichletReg/R/make.VT.R | 44
DirichletReg-0.6-1/DirichletReg/R/plot.DirichletRegData.R | 36
DirichletReg-0.6-1/DirichletReg/R/plot.DirichletRegModel.R | 8
DirichletReg-0.6-1/DirichletReg/R/plot_DRdata_3d.R | 26
DirichletReg-0.6-1/DirichletReg/R/plot_DRdata_4d.R | 59
DirichletReg-0.6-1/DirichletReg/R/predict.DirichletRegModel.R | 12
DirichletReg-0.6-1/DirichletReg/R/print.DirichletRegConfint.R | 12
DirichletReg-0.6-1/DirichletReg/R/print.DirichletRegMixture.R | 2
DirichletReg-0.6-1/DirichletReg/R/print.DirichletRegModel.R | 14
DirichletReg-0.6-1/DirichletReg/R/residuals.DirichletRegModel.R | 20
DirichletReg-0.6-1/DirichletReg/R/summary.DirichletRegData.R | 4
DirichletReg-0.6-1/DirichletReg/R/summary.DirichletRegModel.R | 34
DirichletReg-0.6-1/DirichletReg/R/sysdata.rda |binary
DirichletReg-0.6-1/DirichletReg/R/terms.DirichletRegModel.R | 13
DirichletReg-0.6-1/DirichletReg/R/toTernaryQuaternary.R | 26
DirichletReg-0.6-1/DirichletReg/R/zzz.R | 36
DirichletReg-0.6-1/DirichletReg/build/partial.rdb |binary
DirichletReg-0.6-1/DirichletReg/build/vignette.rds |binary
DirichletReg-0.6-1/DirichletReg/data/ArcticLake.RData |binary
DirichletReg-0.6-1/DirichletReg/data/BloodSamples.RData |binary
DirichletReg-0.6-1/DirichletReg/data/GlacialTills.RData |binary
DirichletReg-0.6-1/DirichletReg/data/ReadingSkills.RData |binary
DirichletReg-0.6-1/DirichletReg/data/Rocks.RData |binary
DirichletReg-0.6-1/DirichletReg/inst/NEWS.Rd | 26
DirichletReg-0.6-1/DirichletReg/inst/NEWS.pdf |only
DirichletReg-0.6-1/DirichletReg/inst/doc/DirichletReg-vig.R | 856 ++++------
DirichletReg-0.6-1/DirichletReg/inst/doc/DirichletReg-vig.Rnw | 38
DirichletReg-0.6-1/DirichletReg/inst/doc/DirichletReg-vig.pdf |binary
DirichletReg-0.6-1/DirichletReg/man/DirichletRegModel.Rd | 42
DirichletReg-0.6-1/DirichletReg/man/ReadingSkills.Rd | 14
DirichletReg-0.6-1/DirichletReg/man/anova.DirichletRegModel.Rd | 2
DirichletReg-0.6-1/DirichletReg/man/dirichreg.Rd | 3
DirichletReg-0.6-1/DirichletReg/src/ddirichlet.c |only
DirichletReg-0.6-1/DirichletReg/src/rdirichlet.c |only
DirichletReg-0.6-1/DirichletReg/src/wght_LL.c |only
DirichletReg-0.6-1/DirichletReg/src/wght_LL_grad_alternative.c |only
DirichletReg-0.6-1/DirichletReg/src/wght_LL_grad_common.c |only
DirichletReg-0.6-1/DirichletReg/tests/testthat/test-ArcticTests_AltPar.R |only
DirichletReg-0.6-1/DirichletReg/tests/testthat/test-ArcticTests_CommPar.R |only
DirichletReg-0.6-1/DirichletReg/tests/testthat/testdata |only
DirichletReg-0.6-1/DirichletReg/vignettes/DirichletReg-vig.Rnw | 38
66 files changed, 1377 insertions(+), 1334 deletions(-)
Title: Functions Useful in the Design and ANOVA of Experiments
Diff between dae versions 2.1-7 dated 2011-07-28 and 2.4-0 dated 2014-12-10
Description: A number of functions that are useful in manipulating factors,
that aid in generating experimental designs and that calculate canonical
efficiency factors for designs. Also there are functions that facilitate
diagnostic checking after an ANOVA, especially when the Error function
has been used in the call to aov.
Author: Chris Brien
Maintainer: Chris Brien
DESCRIPTION | 24 ++++++++++----------
MD5 |only
NAMESPACE | 6 +++++
R/Interaction.ABC.Plot.r | 31 +++++++++++---------------
R/design.plot.r |only
R/extab.r | 2 -
R/fac.functions.r | 28 +++++++++++++----------
R/fac.match.r |only
R/proj.r | 52 +++++++++++++++++++++++++++++++++-----------
R/rmvnorm.r | 34 ++++++++++++++++++----------
inst |only
man/as.numfac.Rd | 21 +++++++++--------
man/blockboundary.plot.Rd |only
man/decomp.relate.Rd | 12 +++++-----
man/design.plot.Rd |only
man/extab.Rd | 21 +++++++++--------
man/fac.ar1mat.Rd | 2 -
man/fac.combine.Rd | 32 ++++++++++++++-------------
man/fac.divide.Rd | 28 +++++++++++------------
man/fac.gen.Rd | 24 ++++++++++----------
man/fac.layout.Rd | 46 ++++++++++++++++++++------------------
man/fac.match.Rd |only
man/fac.meanop.Rd | 16 ++++++-------
man/fac.nested.Rd | 22 +++++++++---------
man/fac.recode.Rd | 14 ++++++-----
man/fac.sumop.Rd | 12 +++++-----
man/fitted.aovlist.Rd | 2 -
man/fitted.errors.rd | 4 +--
man/get.daeTolerance.Rd |only
man/interaction.ABC.plot.Rd | 19 ++++++++--------
man/is.projector.Rd | 10 ++++----
man/mat.I.Rd | 6 ++---
man/mat.J.Rd | 6 ++---
man/mat.ar1.Rd | 8 +++---
man/mat.dirprod.Rd | 12 +++++-----
man/mpone.Rd | 6 ++---
man/print.projector.Rd | 2 -
man/proj2.decomp.Rd | 2 -
man/proj2.ops.Rd | 2 -
man/projector-class.Rd | 2 -
man/projector.Rd | 10 ++++----
man/resid.errors.Rd | 2 -
man/residuals.aovlist.Rd | 2 -
man/rmvnorm.Rd | 24 +++++++++++++-------
man/set.daeTolerance.Rd | 3 +-
man/show-methods.Rd | 2 -
man/strength.Rd | 2 -
47 files changed, 306 insertions(+), 247 deletions(-)
Title: Rcpp bindings for Redis using the hiredis library
Diff between RcppRedis versions 0.1.2 dated 2014-11-06 and 0.1.3 dated 2014-12-10
Description: RcppRedis connects R to the Redis key/value store using the
C client library hiredis
Author: Dirk Eddelbuettel
Maintainer: Dirk Eddelbuettel
ChangeLog | 11 +++++++++++
DESCRIPTION | 8 ++++----
MD5 | 8 ++++----
inst/NEWS.Rd | 14 ++++++++++++++
src/Redis.cpp | 2 +-
5 files changed, 34 insertions(+), 9 deletions(-)
Title: Ensemble platform for species distribution modeling
Diff between biomod2 versions 3.1-48 dated 2014-07-07 and 3.1-64 dated 2014-12-10
Description: Functions for species distribution modeling, calibration and evaluation, ensemble of models.
Author: Wilfried Thuiller, Damien Georges and Robin Engler
Maintainer: Damien Georges
DESCRIPTION | 14 +-
MD5 | 52 +++----
NAMESPACE | 5
NEWS | 7 +
R/BIOMOD_EnsembleForecasting.R | 35 +++--
R/BIOMOD_EnsembleModeling.R | 136 +++++++++++++------
R/BIOMOD_FormatingData.R | 4
R/BIOMOD_Modeling.R | 15 +-
R/BIOMOD_Projection.R | 19 +-
R/BinaryTransformation.R | 24 +++
R/Biomod.Models_RE.R | 24 +--
R/BiomodClass.R | 86 +++++++++---
R/FilteringTransformation.R | 24 +++
R/SampleMat2.R | 3
R/biomod2_models-class.R | 198 +++++++++++++++++++++++-----
R/models_scores_graph.R |only
R/response.plot.R | 3
R/sre.R | 5
R/transform.outputs.R | 10 +
inst/doc/html/00Index.html | 3
man/BIOMOD.models.out-RemoveProperly.Rd | 2
man/BIOMOD.models.out-methods.Rd | 7 +
man/BIOMOD_EnsembleForecasting.Rd | 6
man/BIOMOD_EnsembleModeling.Rd | 2
man/BIOMOD_Modeling.Rd | 2
man/BIOMOD_Projection.Rd | 5
man/ProbDensFunc.Rd | 221 +++++++++++++++++---------------
man/models_scores_graph.Rd |only
28 files changed, 631 insertions(+), 281 deletions(-)
Title: Plot a Model's Response While Varying the Values of the
Predictors
Diff between plotmo versions 2.1.0 dated 2014-11-30 and 2.2.0 dated 2014-12-10
Description: Plot a model's response when varying one or two predictors
while holding the other predictors constant. A poor man's
partial dependence plot.
Author: Stephen Milborrow
Maintainer: Stephen Milborrow
.Rinstignore |only
DESCRIPTION | 6 ++--
MD5 | 34 +++++++++++++-------------
NAMESPACE | 2 -
NEWS | 8 ++++++
R/check.index.R | 40 ++++++++++++++++++-------------
R/grid.R | 4 +--
R/lib.R | 2 -
R/plotmo.R | 10 +++----
R/plotmo.methods.R | 9 +-----
inst/doc/plotmo-notes.pdf |binary
inst/slowtests/test.plotmo.Rout.save | 5 +--
inst/slowtests/test.plotmo.bat | 2 -
inst/slowtests/test.plotmo.center.bat | 2 -
inst/slowtests/test.plotmo.emma.bat | 2 -
inst/slowtests/test.plotmo.fac.Rout.save | 1
inst/slowtests/test.plotmo.fac.bat | 2 -
inst/slowtests/test.plotmo.non.earth.bat | 2 -
man/plotmo.methods.Rd | 10 +++----
19 files changed, 75 insertions(+), 66 deletions(-)
More information about OneArmPhaseTwoStudy at CRAN
Permanent link
Title: Detecting, Combining and Filtering Isotope, Adduct and Homologue
Series Relations in High-Resolution Mass Spectrometry (HRMS)
Data
Diff between nontarget versions 1.5 dated 2014-09-16 and 1.6 dated 2014-12-10
Description: Screening a HRMS data set for peaks related by (1) isotope patterns, (2) different adducts of the same molecule and/or (3) homologue series. The resulting isotopic pattern and adduct groups can then be combined to so-called components, with homologue series information attached. Also allows plotting and filtering HRMS data for mass defects, frequent m/z distances and components vs. non-components.
Author: Martin Loos
Maintainer: Martin Loos
DESCRIPTION | 8 +++----
MD5 | 28 ++++++++++++-------------
NEWS | 4 +++
R/adduct.search.R | 2 -
R/combine.R | 8 ++++---
R/nontarget.R | 2 -
R/pattern.search.R | 4 +--
man/combine.Rd | 52 ++++++++++++++++++++++++++++++++++++++++++++++-
man/deter.iso.Rd | 6 +++--
man/nontarget-package.Rd | 15 ++-----------
man/plotall.Rd | 30 +++++++++++++++++++++++++++
man/plotcomp.Rd | 2 -
man/plotdefect.Rd | 4 +--
man/plotdiff.Rd | 3 --
man/plotgroup.Rd | 6 +----
15 files changed, 124 insertions(+), 50 deletions(-)
Title: Distribution and Equation
Diff between DnE versions 1.01 dated 2013-04-17 and 2.1.0 dated 2014-12-10
Description: The DnE package involves functions to analyse the distribution of a set of given data. The basic idea of the analysis is chi-squared test. Functions which have the form as "is.xxdistribution" are used to analyse whether the data obeys the xxdistrbution. If you do not know which distribution to judge, use function is.dt().
Author: Junyao Chen, Cuiyi He, Boxian Wei
Maintainer: Junyao Chen
DnE-1.01/DnE/R/Cubic.R |only
DnE-1.01/DnE/R/Quart.R |only
DnE-1.01/DnE/man/Cubic.Rd |only
DnE-1.01/DnE/man/Quart.Rd |only
DnE-2.1.0/DnE/DESCRIPTION | 22 ++++---------
DnE-2.1.0/DnE/MD5 | 64 ++++++++++++++++++---------------------
DnE-2.1.0/DnE/R/is.beta.R | 4 +-
DnE-2.1.0/DnE/R/is.binom.R | 4 +-
DnE-2.1.0/DnE/R/is.chisq.R | 2 -
DnE-2.1.0/DnE/R/is.dt.R | 2 -
DnE-2.1.0/DnE/R/is.exp.R | 2 -
DnE-2.1.0/DnE/R/is.f.R | 2 -
DnE-2.1.0/DnE/R/is.gamma.R | 2 -
DnE-2.1.0/DnE/R/is.geom.R | 4 +-
DnE-2.1.0/DnE/R/is.nbinom.R | 4 +-
DnE-2.1.0/DnE/R/is.norm.R | 2 -
DnE-2.1.0/DnE/R/is.pois.R | 4 +-
DnE-2.1.0/DnE/R/is.t.R | 2 -
DnE-2.1.0/DnE/R/is.unif.R | 2 -
DnE-2.1.0/DnE/man/DnE-package.Rd | 15 ++++-----
DnE-2.1.0/DnE/man/is.bern.Rd | 11 +++---
DnE-2.1.0/DnE/man/is.beta.Rd | 15 ++++-----
DnE-2.1.0/DnE/man/is.binom.Rd | 17 ++++------
DnE-2.1.0/DnE/man/is.chisq.Rd | 15 ++++-----
DnE-2.1.0/DnE/man/is.degen.Rd | 11 +++---
DnE-2.1.0/DnE/man/is.dt.Rd | 16 ++++-----
DnE-2.1.0/DnE/man/is.exp.Rd | 15 ++++-----
DnE-2.1.0/DnE/man/is.f.Rd | 15 ++++-----
DnE-2.1.0/DnE/man/is.gamma.Rd | 13 +++----
DnE-2.1.0/DnE/man/is.geom.Rd | 15 ++++-----
DnE-2.1.0/DnE/man/is.nbinom.Rd | 17 ++++------
DnE-2.1.0/DnE/man/is.norm.Rd | 15 ++++-----
DnE-2.1.0/DnE/man/is.pois.Rd | 13 +++----
DnE-2.1.0/DnE/man/is.t.Rd | 15 ++++-----
DnE-2.1.0/DnE/man/is.unif.Rd | 15 ++++-----
35 files changed, 165 insertions(+), 190 deletions(-)
Title: Export Decomposition (Wang-Wei-Zhu and source)
Diff between decompr versions 1.2 dated 2014-08-29 and 1.3.2 dated 2014-12-10
Description: decompr implements two export decomposition algorithms. Firstly,
the Wang-Wei-Zhu (Wang, Wei, and Zhu 2013) algorithm splits bilateral gross
exports into 16 value added components. Secondly, the Source decomposition
algorithm derives the value added origin of exports by country and
industry, which is also based on Wang, Wei, and Zhu (2013).
Author: Bastiaan Quast [aut, cre],
Fei Wang [aut],
Victor K
Maintainer: Bastiaan Quast
DESCRIPTION | 26 +++---
MD5 | 36 +++++---
NAMESPACE | 3
NEWS | 24 +++++
R/decompr.R | 30 +++++++
R/load_tables.R | 185 +++------------------------------------------
R/load_tables_vectors.R |only
R/wwz.R | 2
README.md | 2
data/wiod2.rda |only
inst/CITATION | 21 ++---
man/decomp.Rd | 2
man/decompr.Rd | 4
man/final_demand.Rd | 2
man/industry_names.Rd |only
man/intermediate_demand.Rd | 2
man/kung_fu.Rd | 2
man/load_tables.Rd | 2
man/load_tables_vectors.Rd |only
man/output.Rd |only
man/region_names.Rd |only
man/wwz.Rd | 2
22 files changed, 127 insertions(+), 218 deletions(-)
Title: Mapping Smoothed Effect Estimates from Individual-Level Data
Diff between MapGAM versions 0.7-0 dated 2013-12-12 and 0.7-4 dated 2014-12-10
Description: Contains functions for mapping odds ratios or other effect estimates using individual-level data such as case-control study data, using generalized additive models (GAMs) for smoothing with a two-dimensional predictor (e.g., geolocation or exposure to chemical mixtures) while adjusting for confounding variables, using methods described by Kelsall and Diggle (1998) and Webster at al. (2006). Includes convenient functions for mapping, efficient control sampling, and permutation tests for the null hypothesis that the two-dimensional predictor is not associated with the outcome variable (adjusting for confounders).
Author: Veronica Vieira, Scott Bartell, and Robin Bliss
Maintainer: Scott Bartell
ChangeLog | 14 +++++++
DESCRIPTION | 11 +++--
MD5 | 22 +++++------
NAMESPACE | 4 +-
R/colormap.R | 96 +++++++++++++++++++++++++++++---------------------
R/sampcont.R | 5 +-
R/trimdata.R | 20 ++++++----
man/MapGAM-package.Rd | 6 +--
man/colormap.Rd | 26 ++++++++-----
man/modgam.Rd | 26 ++++++-------
man/sampcont.Rd | 2 -
man/trimdata.Rd | 2 -
12 files changed, 141 insertions(+), 93 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2013-10-26 1.1
2013-08-11 1.0
Title: Nonparametric Simulation of RNA-Seq Data
Diff between SimSeq versions 1.0.0 dated 2014-02-18 and 1.2.0 dated 2014-12-10
Description: RNA sequencing analysis methods are often derived by relying on hypothetical parametric models for read counts that are not likely to be precisely satisfied in practice. Methods are often tested by analyzing data that have been simulated according to the assumed model. This testing strategy can result in an overly optimistic view of the performance of an RNA-seq analysis method. We develop a data-based simulation algorithm for RNA-seq data. The vector of read counts simulated for a given experimental unit has a joint distribution that closely matches the distribution of a source RNA-seq dataset provided by the user. Users control the proportion of genes simulated to be differentially expressed (DE) and can provide a vector of weights to control the distribution of effect sizes. The algorithm requires a matrix of RNA-seq read counts with large sample sizes in at least two treatment groups. Many datasets are available that fit this standard.
Author: Samuel Benidt
Maintainer: Samuel Benidt
DESCRIPTION | 12 +--
MD5 | 21 ++---
NAMESPACE | 1
NEWS | 10 ++
R/SimData.R | 48 +++++++++---
R/SortData.R | 2
data/datalist |only
data/kidney.rda |binary
demo/SimSeq.R | 85 +++++++++++++++++++---
man/SimData.Rd | 186 +++++++++++++++++++++++++++++++++++++++++++++++---
man/SimSeq-package.Rd | 6 -
man/kidney.Rd | 177 ++++++++++++++++++++++++++++++++++++++++++++++-
12 files changed, 492 insertions(+), 56 deletions(-)
Title: Seawater Carbonate Chemistry with R
Diff between seacarb versions 3.0.2 dated 2014-11-18 and 3.0.3 dated 2014-12-10
Description: Calculates parameters of the seawater carbonate system and assists the design of ocean acidification perturbation experiments.
Author: Jean-Pierre Gattuso [aut, cre, cph],
Jean-Marie Epitalon [aut],
Heloise Lavigne [aut],
James Orr [ctb],
Bernard Gentili [ctb],
Andreas Hofmann [ctb],
Aurélien Proye [ctb],
Karline Soetaert [ctb],
James Rae [ctb]
Maintainer: Jean-Pierre Gattuso
ChangeLog | 8 ++++++
DESCRIPTION | 10 +++----
MD5 | 66 +++++++++++++++++++++++++-------------------------
R/Om.R | 2 -
R/bor.R | 74 ++++++++++++++++++++++++++++-----------------------------
R/buffer.R | 28 ++++++++++-----------
R/buffesm.R | 2 -
R/carb.R | 28 ++++++++++-----------
R/oa.R | 2 -
R/pCa.R | 2 -
R/pHinsi.R | 2 -
R/pTA.R | 4 +--
R/pgas.R | 4 +--
R/pmix.R | 2 -
R/psi.R | 8 +++---
man/K0.Rd | 4 +--
man/Om.Rd | 8 +++---
man/bor.Rd | 2 -
man/buffer.Rd | 10 ++++---
man/buffesm.Rd | 10 ++++---
man/carb.Rd | 28 +++++++++++----------
man/f2pCO2.Rd | 6 +++-
man/oa.Rd | 8 +++---
man/p2fCO2.Rd | 8 ++++--
man/p2xCO2.Rd | 6 +++-
man/pCa.Rd | 15 +++++++----
man/pHconv.Rd | 2 -
man/pHinsi.Rd | 6 +++-
man/pTA.Rd | 18 ++++++++++---
man/pgas.Rd | 12 ++++++---
man/pmix.Rd | 12 ++++++---
man/ppH.Rd | 6 +++-
man/psi.Rd | 13 ++++++----
man/x2pCO2.Rd | 10 ++++---
34 files changed, 244 insertions(+), 182 deletions(-)
Title: R Commander
Diff between Rcmdr versions 2.1-4 dated 2014-10-30 and 2.1-5 dated 2014-12-10
Description:
A platform-independent basic-statistics GUI (graphical user interface) for R, based on the tcltk package.
Author: John Fox [aut, cre],
Milan Bouchet-Valat [aut],
Liviu Andronic [ctb],
Michael Ash [ctb],
Theophilius Boye [ctb],
Stefano Calza [ctb],
Andy Chang [ctb],
Philippe Grosjean [ctb],
Richard Heiberger [ctb],
Kosar Karimi Pour [ctb],
G. Jay Kerns [ctb],
Renaud Lancelot [ctb],
Matthieu Lesnoff [ctb],
Uwe Ligges [ctb],
Samir Messad [ctb],
Martin Maechler [ctb],
Robert Muenchen [ctb],
Duncan Murdoch [ctb],
Erich Neuwirth [ctb],
Dan Putler [ctb],
Brian Ripley [ctb],
Miroslav Ristic [ctb],
Peter Wolf [ctb],
Kevin Wright [ctb]
Maintainer: John Fox
DESCRIPTION | 12
MD5 | 20
NAMESPACE | 6
NEWS | 8
R/distributions-menu.R | 1
inst/po/ca/LC_MESSAGES/R-Rcmdr.mo |binary
inst/po/sl/LC_MESSAGES/R-Rcmdr.mo |binary
man/Rcmdr-package.Rd | 4
man/Rcmdr.Utilities.Rd | 4
po/R-ca.po | 9107 +++++++++++++++++++-------------------
po/R-sl.po | 96
11 files changed, 4648 insertions(+), 4610 deletions(-)
Title: R Interface to the USGS BISON API
Diff between rbison versions 0.4.3 dated 2014-10-15 and 0.4.5 dated 2014-12-10
Description: Interface to the USGS BISON API, a database for
species occurrence data on the web. Data comes from species in the
United States, from participating data providers. This package
focuses mostly on getting data from BISON, via taxonomic and location
based queries. A simple function is provided to help visualize data.
Author: Scott Chamberlain [aut, cre]
Maintainer: Scott Chamberlain
rbison-0.4.3/rbison/tests/test-all.R |only
rbison-0.4.5/rbison/DESCRIPTION | 24 -
rbison-0.4.5/rbison/MD5 | 43 +--
rbison-0.4.5/rbison/NAMESPACE | 1
rbison-0.4.5/rbison/NEWS | 10
rbison-0.4.5/rbison/R/bison.R | 16 -
rbison-0.4.5/rbison/R/bison_providers.R | 16 -
rbison-0.4.5/rbison/R/bison_solr.R | 32 +-
rbison-0.4.5/rbison/R/bison_stats.R | 2
rbison-0.4.5/rbison/R/bison_tax.R | 40 +--
rbison-0.4.5/rbison/R/bisonmap.R | 48 +--
rbison-0.4.5/rbison/README.md | 186 +++++++-------
rbison-0.4.5/rbison/build/vignette.rds |binary
rbison-0.4.5/rbison/inst/readmeimg/unnamed-chunk-10-1.png |only
rbison-0.4.5/rbison/inst/readmeimg/unnamed-chunk-13-1.png |only
rbison-0.4.5/rbison/inst/readmeimg/unnamed-chunk-14-1.png |only
rbison-0.4.5/rbison/inst/readmeimg/unnamed-chunk-15-1.png |only
rbison-0.4.5/rbison/inst/readmeimg/unnamed-chunk-19-1.png |only
rbison-0.4.5/rbison/inst/readmeimg/unnamed-chunk-7-1.png |only
rbison-0.4.5/rbison/man/bison.Rd | 73 -----
rbison-0.4.5/rbison/man/bison_solr.Rd | 51 ---
rbison-0.4.5/rbison/man/bison_stats.Rd | 2
rbison-0.4.5/rbison/man/bison_tax.Rd | 2
rbison-0.4.5/rbison/man/bisonmap.Rd | 2
rbison-0.4.5/rbison/tests/testthat/Rplots.pdf |binary
rbison-0.4.5/rbison/tests/testthat/test-bisonmap.R | 9
26 files changed, 230 insertions(+), 327 deletions(-)
Title: Convert R Graphics to Flash Animations
Diff between R2SWF versions 0.8 dated 2014-02-23 and 0.8-1 dated 2014-12-10
Description: This package uses the Ming library
(http://www.libming.org/) to create Flash animations.
Users can either use the SWF device swf() to generate SWF file
directly through plotting functions like plot() and lines(),
or convert images of other formats (SVG, PNG, JPEG) into SWF.
Author: Yixuan Qiu, Yihui Xie, Cameron Bracken and authors of included
software. See file AUTHORS for details.
Maintainer: Yixuan Qiu
DESCRIPTION | 10 +++++-----
MD5 | 23 ++++++++++++-----------
NEWS | 10 ++++++++++
R/svg2swf.R | 15 +++++++++++++++
README.md |only
man/dev2swf.Rd | 42 ++++++++++++++++++------------------------
man/file2swf.Rd | 16 ++++++++--------
man/image2swf.Rd | 25 +++++++++++--------------
man/svg2swf.Rd | 30 ++++++++++++++----------------
man/swf.Rd | 24 +++++++++++-------------
man/swf2html.Rd | 19 +++++++++----------
src/svg2swf.c | 6 +++---
src/swfDevice.c | 4 ++++
13 files changed, 120 insertions(+), 104 deletions(-)
Title: Functional time series analysis
Diff between ftsa versions 4.0 dated 2014-06-23 and 4.1 dated 2014-12-10
Description: Functions for functional time series
Author: Rob J Hyndman and Han Lin Shang
Maintainer: Shang H.
ChangeLog | 6 ++++++
DESCRIPTION | 10 +++++-----
MD5 | 30 +++++++++++++++---------------
NAMESPACE | 2 ++
build/vignette.rds |binary
man/dynupdate.Rd | 4 +---
man/forecast.ftsm.Rd | 2 +-
man/fplsr.Rd | 8 +++++---
man/ftsa-package.Rd | 9 +++++----
man/ftsm.Rd | 2 +-
man/ftsmiterativeforecasts.Rd | 2 +-
man/mean.fts.Rd | 4 ++--
man/median.fts.Rd | 4 ++--
man/pcscorebootstrapdata.Rd | 6 +++---
man/sd.fts.Rd | 4 ++--
man/var.fts.Rd | 4 ++--
16 files changed, 53 insertions(+), 44 deletions(-)
Title: Utility Functions For GATK
Diff between gsalib versions 2.0 dated 2013-07-03 and 2.1 dated 2014-12-10
Description: This package contains utility functions used by the Genome Analysis Toolkit (GATK) to load tables and plot data. The GATK is a toolkit for variant discovery in high-throughput sequencing data.
Author: Kiran Garimella
Maintainer: Geraldine Van der Auwera
gsalib-2.0/gsalib/doc |only
gsalib-2.1/gsalib/DESCRIPTION | 15 +++++++--------
gsalib-2.1/gsalib/LICENSE |only
gsalib-2.1/gsalib/MD5 | 8 ++++----
gsalib-2.1/gsalib/man/gsalib-package.Rd | 6 +++---
gsalib-2.1/gsalib/man/test_gatkreport.table.Rd | 2 +-
6 files changed, 15 insertions(+), 16 deletions(-)
Title: Effect Displays for Linear, Generalized Linear, and Other Models
Diff between effects versions 3.0-2 dated 2014-11-25 and 3.0-3 dated 2014-12-10
Description:
Graphical and tabular effect displays, e.g., of interactions, for
various statistical models with linear predictors.
Author: John Fox [aut, cre],
Sanford Weisberg [aut],
Michael Friendly [aut],
Jangman Hong [aut],
Robert Andersen [ctb],
David Firth [ctb],
Steve Taylor [ctb]
Maintainer: John Fox
DESCRIPTION | 18 -
MD5 | 40 +--
NAMESPACE | 4
NEWS | 8
R/Effect.R | 176 ---------------
R/effectsmer.R | 9
R/plot-methods.R | 522 +----------------------------------------------
R/plot.effpoly.R | 24 +-
data/Arrests.rda |binary
data/BEPS.rda |binary
data/Cowles.rda |binary
data/Hartnagel.rda |binary
data/Prestige.rda |binary
data/TitanicSurvival.rda |binary
data/WVS.rda |binary
data/Wells.rda |binary
man/BEPS.Rd | 17 -
man/WVS.Rd | 19 -
man/effect.Rd | 32 +-
man/effects-package.Rd | 8
man/summary.effect.Rd | 19 -
21 files changed, 130 insertions(+), 766 deletions(-)
Title: Create Cryptographic Hash Digests of R Objects
Diff between digest versions 0.6.5 dated 2014-12-09 and 0.6.6 dated 2014-12-10
Description: Implementation of a function 'digest()' for the creation
of hash digests of arbitrary R objects (using the md5, sha-1, sha-256,
crc32 and xxhash algorithms) permitting easy comparison of R language
objects, as well as a function 'hmac()' to create hash-based message
authentication code.
The md5 algorithm by Ron Rivest is specified in RFC 1321, the sha-1
and sha-256 algorithms are specified in FIPS-180-1 and FIPS-180-2,
and the crc32 algorithm is described in
ftp://ftp.rocksoft.com/cliens/rocksoft/papers/crc_v3.txt.
For md5, sha-1, sha-256 and aes, this package uses a small standalone
implementations that were provided by Christophe Devine. For crc32, code
from the zlib library is used. For sha-512, an implementation by Aaron
D. Gifford is used. For xxHash, the implementation by Yann Collet is used.
Please note that this package is not meant to be deployed for
cryptographic purposes for which more comprehensive (and widely
tested) libraries such as OpenSSL should be used.
Author: Dirk Eddelbuettel
Maintainer: Dirk Eddelbuettel
ChangeLog | 13 ++++++++++++-
DESCRIPTION | 8 ++++----
MD5 | 6 +++---
src/digest.c | 13 +++++++------
4 files changed, 26 insertions(+), 14 deletions(-)
Title: Tools for processing COPAS large-particle flow cytometer data
Diff between COPASutils versions 0.1.4 dated 2014-10-05 and 0.1.5 dated 2014-12-10
Description: A logical workflow for the reading, processing, and visualization
of data obtained from the Union Biometrica Complex Object Parametric
Analyzer and Sorter (COPAS) platform large-particle flow cytometers and a
powerful suite of functions for the rapid processing and analysis of large
high-throughput screening data sets. It combines the speed of dplyr with
the elegance of ggplot2 to make analysis of COPAS data fast and painless.
Author: Tyler Shimko
Maintainer: Erik Andersen
DESCRIPTION | 6 ++---
MD5 | 8 +++----
R/COPASutils_functions.R | 1
data/bubbleSVMmodel_noProfiler.RData |binary
inst/doc/Overview.html | 36 +++++++++++++++++------------------
5 files changed, 26 insertions(+), 25 deletions(-)
Title: Causal Inference Test
Diff between cit versions 1.2 dated 2013-12-20 and 1.3 dated 2014-12-10
Description: This package implements a formal statistical hypothesis test, resulting in a p-value, to quantify uncertainty in a causal inference pertaining to a measured factor, e.g. a molecular species, which potentially mediates a known causal association between a locus and a quantitative trait. The test is applicable to data that includes genotype (discrete), possible causal mediator such as gene expression (continuous) and an outcome of interest (continuous).
Author: Joshua Millstein
Maintainer: Joshua Millstein
cit-1.2/cit/src/cit_v5.cpp |only
cit-1.3/cit/DESCRIPTION | 8 ++++----
cit-1.3/cit/MD5 | 6 +++---
cit-1.3/cit/man/cit-package.Rd | 4 ++--
cit-1.3/cit/src/cit_v6.cpp |only
5 files changed, 9 insertions(+), 9 deletions(-)
Title: Bayesian Analysis of Generalized Elliptical Semi-parametric
Models
Diff between BayesGESM versions 1.0 dated 2014-05-08 and 1.1 dated 2014-12-10
Description: This package allows obtain the statistical inference based on Bayesian approach for regression models under the assumption that independent additive errors follow normal, Student-t, slash, contaminated normal, Laplace or symmetric hyperbolic distribution, where both location and dispersion parameters of the response variable distribution include non-parametric additive components described by B-splines using the function BayesGESM and it also allows to obtain the statistical inference based on Bayesian approach for flexible measurement error models using the function fmem.
Author: Luz Marina Rondon
Maintainer: Luz Marina Rondon
BayesGESM-1.0/BayesGESM/R/BayesGESM-internal.R |only
BayesGESM-1.1/BayesGESM/DESCRIPTION | 14 ++--
BayesGESM-1.1/BayesGESM/MD5 | 21 ++++--
BayesGESM-1.1/BayesGESM/NAMESPACE | 4 -
BayesGESM-1.1/BayesGESM/R/BayesGESM.R | 30 ++++-----
BayesGESM-1.1/BayesGESM/R/bsp.R |only
BayesGESM-1.1/BayesGESM/R/fmem.R |only
BayesGESM-1.1/BayesGESM/R/mcmc.fmem.R |only
BayesGESM-1.1/BayesGESM/R/summary.fmem.R |only
BayesGESM-1.1/BayesGESM/man/BayesGESM-package.Rd | 33 ++++++---
BayesGESM-1.1/BayesGESM/man/BayesGESM.Rd | 76 +++++++++++------------
BayesGESM-1.1/BayesGESM/man/bsp.Rd |only
BayesGESM-1.1/BayesGESM/man/fmem.Rd |only
BayesGESM-1.1/BayesGESM/man/mcmc.Rd | 2
BayesGESM-1.1/BayesGESM/man/mcmc.fmem.Rd |only
BayesGESM-1.1/BayesGESM/man/summary.fmem.Rd |only
16 files changed, 98 insertions(+), 82 deletions(-)